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  • Classify Sequences with Kraken

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Input data

To classify single-end (SE) reads or scaffoldscontigs, received by reads de novo assembly, set this parameter to "SE reads or scaffoldscontigs".
To classify paired-end (PE) reads, set the value to "PE reads".
One or two slots of the input port are used depending on the value of the parameter. Pass URL(s) to data to these slots.
The input files should be in FASTA or FASTQ formats.

 SE reads or scaffoldscontigs

A path to the folder with the Kraken database files.

Quick operation

Stop classification of an input read after the certain number of hits.
The value can be specified in the "Minimum number of hits" parameter.

Load database into memory

Load the Kraken database into RAM (--preload).
This can be useful to improve the speed. The database size should be less than the RAM size.
The other option to improve the speed is to store the database on ramdisk. Set this parameter to "False" in this case.

Number of threads

Use multiple threads (--threads).

Output file

Specify the output file name.


Parameters in Workflow File


The element has 1 input port:

Name in GUI: Input sequences: 

URL(s) to FASTQ or FASTA file(s) should be provided. In case of SE reads or scaffolds contigs use the "Input URL 1" slot only.

In case of PE reads input "left" reads to "Input URL 1", "right" reads to "Input URL 2". See also the "Input data" parameter of the element.

Name in Workflow File: in


SlotInGUISlot in Workflow FileType
Input URLurlstring

The element has 1 output port:

Name in GUI: Kraken Classification


A map of sequence names with the associated taxonomy IDs, classified by Kraken.

Name in Workflow File: out


SlotInGUISlot in Workflow FileType
Taxonomy classification data